- 1. Data and associated plots based on the Ct values
- 2. Data and associated plots based on the Negative Delta Ct values [log normalized]
- 2.1 Delta Ct value - Data table
- 2.2 Negative Delta Ct value [log normalized] - Data table
- 2.3 Box Plot - Negative Delta Ct values [log normalized] of all samples based on ‘sample plate effect’
- 2.4 Density Plot - Negative DCt Values [log normalized] of all samples’
- 2.5 Density Plot - Negative Delta Ct Values [log normalized] of all samples based on ‘sample plate effect’ - color fill
- 2.6 Density Plot - Negative Delta Ct Values [log normalized] of all samples’ based on ‘sample plate effect’ - semi-transparent fill
- 2.7 Scree Plot to determine No. of PCs - Negative Delta Ct Values [log normalized] of all samples
- 2.8 PCA Plot - Negative Delta Ct Values [log normalized] of all samples based on ‘sample plate effect + type’
- 2.9 PCA Plot - Negative Delta Ct Values [log normalized] of all samples based on ‘type + timepoints’
- 2.10 PCA Plot with ellipse - Negative Delta Ct Values [log normalized] of all samples based on ‘type + timepoints’
- 2.11 PCA Plot with ellipse - Negative Delta Ct Values [log normalized] of all samples based on ‘timepoints + type’
- 2.12 Delta Delta Ct (Covid-19 vs. Healthy Control) - Data table
- 2.13 Fold Change - Linear (Covid-19 vs. Healthy Control) - Data table
- 2.14 Fold Change - Inverse Scale (Covid-19 vs. Healthy Control) - Data table
- 2.15 Fold Change - Log Scale (Covid-19 vs. Healthy Control) - Data table
- 2.16 Delta Delta Ct [Covid-19 (TP1, TP2, TP3, TP4 ] vs. [Healthy Control (TP1)] - Data table
- 2.17 Fold Change - Linear [Covid-19 (TP1, TP2, TP3, TP4 ] vs. [Healthy Control (TP1)] - Data table
- 2.18 Fold Change - Inverse Scale [Covid-19 (TP1, TP2, TP3, TP4 ] vs. [Healthy Control (TP1)] - Data table
- 2.19 Fold Change - Log Scale [Covid-19 (TP1, TP2, TP3, TP4 ] vs. [Healthy Control (TP1)] - Data table
- 2.20 Statistical Analysis from limma on Negative Delta Ct (log normalized)- between Covid-19 vs. Healthy Control - Data table
- 2.21 Venn Diagram - between Covid-19 vs. Healthy Control - Data table
- 2.22 Statistical Analysis from limma on Negative Delta Ct (log normalized)- between [Covid-19 (TP1, TP2, TP3, TP4 ] vs. [Healthy Control (TP1)] - Data table
- 2.23 Venn Diagram from limma - between [Covid-19 (TP1, TP2, TP3, TP4 ] vs. [Healthy Control (TP1)] - Data table
- 3. Data and associated plots based on the Negative Delta Ct values [log normalized] - Batch Corrected (ComBat function from SVA- R Package)
1. Data and associated plots based on the Ct values
1.4 Box Plot - Ct values of Housekeeping Genes based on ‘sample plate effect’

1.5 Box Plot - Ct values of all samples based on ‘sample plate effect’

1.6 Density Plot - Ct values of all samples’

1.7 Density Plot - Ct values of all samples based on ‘sample plate effect’ - color fill

1.8 Density Plot - Ct values of all samples’ based on ‘sample plate effect’ - semi-transparent fill

1.9 Scree Plot to determine No. of PCs - Ct values of all samples

1.10 PCA Plot - Ct values of all samples based on ‘sample plate effect + type’



1.11 PCA Plot - Ct values of all samples based on ‘type + timepoints’



1.12 PCA Plot with ellipse - Ct values of all samples based on ‘type + timepoints’



1.13 PCA Plot with ellipse - Ct values of all samples based on ‘timepoints + type’



2. Data and associated plots based on the Negative Delta Ct values [log normalized]
2.3 Box Plot - Negative Delta Ct values [log normalized] of all samples based on ‘sample plate effect’

2.4 Density Plot - Negative DCt Values [log normalized] of all samples’

2.5 Density Plot - Negative Delta Ct Values [log normalized] of all samples based on ‘sample plate effect’ - color fill

2.6 Density Plot - Negative Delta Ct Values [log normalized] of all samples’ based on ‘sample plate effect’ - semi-transparent fill

2.7 Scree Plot to determine No. of PCs - Negative Delta Ct Values [log normalized] of all samples

2.8 PCA Plot - Negative Delta Ct Values [log normalized] of all samples based on ‘sample plate effect + type’



2.9 PCA Plot - Negative Delta Ct Values [log normalized] of all samples based on ‘type + timepoints’



2.10 PCA Plot with ellipse - Negative Delta Ct Values [log normalized] of all samples based on ‘type + timepoints’



2.11 PCA Plot with ellipse - Negative Delta Ct Values [log normalized] of all samples based on ‘timepoints + type’



2.21 Venn Diagram - between Covid-19 vs. Healthy Control - Data table

2.23 Venn Diagram from limma - between [Covid-19 (TP1, TP2, TP3, TP4 ] vs. [Healthy Control (TP1)] - Data table

3. Data and associated plots based on the Negative Delta Ct values [log normalized] - Batch Corrected (ComBat function from SVA- R Package)
3.2 Box Plot - Negative Delta Ct values [log normalized] - Batch Correction of all samples based on ‘sample plate effect’

3.3 Density Plot - Negative DCt Values [log normalized] - Batch Correction of all samples’

3.4 Density Plot - Negative Delta Ct Values [log normalized] - Batch Correction of all samples based on ‘sample plate effect’ - color fill

3.5 Density Plot - Negative Delta Ct Values [log normalized] - Batch Correction of all samples’ based on ‘sample plate effect’ - semi-transparent fill

3.6 Scree Plot to determine No. of PCs - Negative Delta Ct Values [log normalized] - Batch Correction of all samples

3.7 PCA Plot - Negative Delta Ct Values [log normalized] - Batch Correction of of all samples based on ‘sample plate effect + type’



3.8 PCA Plot - Negative Delta Ct Values [log normalized] - Batch Correction of all samples based on ‘type + timepoints’



3.9 PCA Plot with ellipse - Negative Delta Ct Values [log normalized] - Batch Correction of all samples based on ‘type + timepoints’



3.10 PCA Plot with ellipse - Negative Delta Ct Values [log normalized] - Batch Correction of all samples based on ‘timepoints + type’



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